分子动力学软件选择.docx

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1、分子动力学软件选择分子动力学软件选择TherearewidelyusedpackageslikeAMBER,CHARMmandX-PLORhttpdocsj/doc/1385f5d0360cba1aa811daff./amber/amber.httpdocsj/doc/1385f5d0360cba1aa811daff./httpdocsj/doc/1385f5d0360cba1aa811daff./CHARMmandX-PLORbothusethesameforcefield.Ambersisdifferent.IfyoureWintel-bound,youcouldtryHyperchem,

2、whichhasafreedownloadabledemo:httpdocsj/doc/1385f5d0360cba1aa811daff./products/hc5_features.Ithasanicestructurebuildcapability(theotherpackageshavepowerfullanguages,butcanbeintimidatingtonewusers).OpenSourceadherentscanfindawealthoffreepackagesatSAL,anexcellentsite:httpdocsj/doc/1385f5d0360cba1aa811

3、daff./Z/2/index.sMypersonalfavouritesareMMTK,EGOandVMD/NAMD.Icompiledalistoffreeandcommericalprogramsathttpdocsj/doc/1385f5d0360cba1aa811daff./chemistry/soft_mod_en.modelinginsolutionispossiblee.g.withtheseprograms(tothebestofmyknowledge):commercial:AMSOL,GROMOS,Titanfree:GAMESOL,GROMACS,MOIL,OMNISO

4、L,TinkerYoufindlinkstoalloftheseprogramsathttpdocsj/doc/1385f5d0360cba1aa811daff./chemistry/soft_mod_en.PAPA(计算粒状物料的三维并行分子动力学计算程序)【URL】httpica1.uni-stuttgart.de/Research/Software_P3T/papa.【作者】ICA1Group,InstituteofComputerApplications(ICA)oftheUniversityofStuttgart【语言版本】English【收费情况】免费【用处】Characteris

5、tic:dissipativeinteractionforrotating,rough,sphericalparticlesgeometryelements:walls,cylinders,spheres,etcfreelyconfigurablematerialpropertiesofwallsandparticlesfreelyconfigurableforanarbitraynumberofmaterialsobjectoriented,writteninC+fullcheckpointingsupportedseveralcompilationoptions:supportofX11g

6、raphics,reductionto2D,debuggingaids,etc.Applications:simulationofgranularmedia,silofillingandsteadyflowproblems,spherepackingsofmono-andpolydispersesystemProtoMol(分子动力学并行计算软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./lcls/Protomol.【作者】LCLSGroupattheUniversityofNotreDame【语言版本】English【操作系统】SunOS5.8

7、,IRIX6.5,Linux2.4,AIX5.1【收费情况】免费【用处】PROTOMOLisanobject-orientedcomponentbasedframeworkformoleculardynamicssimulations.TheframeworksupportstheCHARMM19and28a2forcefieldsandisabletoprocessPDB,PSF,XYZandDCDtrajectoryfiles.Itisdesignedforhighflexibility,easyextendibilityandmaintenance,andhighperformanced

8、emands,includingparallelization.Thetechniqueofmultipletime-steppinghasbeenusedtoimprovelong-termefficiency,andtheuseoffastelectrostaticforceevaluationalgorithmslikeplainEwald,ParticleMeshEwald,andMultigridsummationfurtherimprovesperformance.LongertimestepsarepossibleusingMOLLY,LangevinMollyandHybrid

9、MonteCarlo,Nose-Hoover,andLangevinintegrators.Inaddition,PROTOMOLhasbeendesignedtointeractwithVMD,avisualizationenginedevelopedbytheUniversityofIllinoisthatisusedfordisplayinglargebiomolecularsystemsinthreedimensions.PROTOMOLisfreedistributedsoftware,andthesourcecodeisincluded.【相关链接】VMD(分子可视化软件)美国圣母

10、大学：计算生命科学实验室Claessen站点的分子模型化软件【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./chemistry/soft_mod_en.【简介】MolecularModelingCommercialSoftware3DViewer:converts2Dstructuresinto3DwithsimpleMM2Alchemy2000:semiempirical,QSAR,Protein,Polymer,LogPAMPAC:semiempiricalquantummechanicalprogramAMSOL:semiempirical,so

11、lvationmodelsforfreeenergiesofsolvationinaqueoussolutionsandinalkanesolventsPersonalCAChe:visualizemoleculesin3D,searchforconformations,analyzechemicalreactivityandpredictpropertiesofcompoundsQuantumCAChe:PersonalCaCheplusmoleculardynamicsandsemi-empiricalMOPACandZINDOquantummechanicsChem3D:MOPACand

12、Gaussianintegration,ChemProp,.Gaussian98W:MP2,MP3,MP4,MP5,HF,CASSCF,GVB,QCISD,BD,CCSD,G1,G2,ZINDO,ONIOMcalculations,DFTexcitedstates,VCDintensities,.GROMOS:general-purposemoleculardynamicscomputersimulationpackageforthestudyofbiomolecularsystemsHyperchemSuite:semiempirical,RMSFit,MoleculePresentatio

13、ns,SequenceEditor,CrystalBuilder,SugarBuilder,ConformationalSearch,QSARProperties,ScriptEditor.(HyperchemPro,HyperchemStd.)Jaguar:electronicstructurecalculationMacroModel:allowsthegraphicalconstructionofcomplexchemicalstructuresmechanicsanddynamicstechniquesinvacuoorinsolutionMOPAC2000:thelatestvers

14、ionofMOPACSpartan:MM,semiempirical,abinitio,DFT,.Titan:TITANistheunionofWavefunctionsversatile,easy-to-useinterfacewithfast,computationalalgorithmsfromSchr鰀ingersJaguarWinMOPAC:basedonMOPACShareware/Freeware3DViewerforISISDraw:converts2Dstructuresinto3DwithsimpleMM2Biomer:onlinejavaapplet,modelbuild

15、ersforpolynucleotides(DNA/RNA),polysaccharidesandproteins,interactivemoleculeeditor,AMBERforce-fieldbasedgeometryoptimization,simulatedannealingwithmoleculardynamics,andtheabilitytosavegif,jpeg,andppmimagesChem3DNet:demoversionofChem3DCOLUMBUS:high-levelabinitiomolecularelectronicstructurecalculatio

16、nsDalton:quantumchemistryprogramGAMESOL:calculatefreeenergiesofsolvationbasedonfixed,gas-phasesolutegeometriesinterfacingGAMESSGAMESS:GeneralAtomicandMolecularElectronicStructureSystemisageneralabinitioquantumchemistrypackageGaussianBasisSet:getanyGaussianbasissetyoucanimagineGROMACS:fullyautomatedt

17、opologybuilderforproteins,moleculardynamics,leap-frogintegrator,positionlangevindynamics,normalmodeanalysis,electrostatics,non-equilibriumMD,NMRrefinementwithNOEdata,largenumberofpowerfulanalysistools,.Hckel:constructstheHckelmatrix,theprogramsthencalculate,displayMOIL:molecularmodeling,energyminimi

18、zationandmoleculardynamicssimulationforbiomoleculeslikeproteinsMoldy:moleculardynamicssimulationprogram,liquids,solids,rigidsurfacesMOPAC:generalpurposesemiempiricalmolecularorbitalpackageforthestudyofchemicalstructuresandreactionsMOPAC5.08mn:modifiedversionofMOPACNWChem:quantumpackageforsupercomput

19、ersandLinux,SCF,RHF,UHF,DFT,CASSCF,interfacetoPythonprogramminglanguageOMNISOL:calculatingfreeenergiesofsolvationfororganicmoleculescontainingH,C,N,O,F,S,Cl,Br,andIinwaterandorganicsolventsPCGAMESS:GAMESSfortheIntelcommunityQ:moleculardynamicspackagedesignedforfreeenergycalculationsinbiomolecularsys

20、temTinker:molecularmodelingsoftwareisacompleteandgeneralpackageformolecularmechanicsanddynamicsVMD(分子可视化软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./Research/vmd/【作者】BiophysicsGroup,UniversityofIllinoisatUrbana-Champaign(UIUC)【语言版本】English【收费情况】免费【用处】VMDisamolecularvisualizationprogramfordisplayi

21、ng,animating,andanalyzinglargebiomolecularsystemsusing3-Dgraphicsandbuilt-inscripting.VMDsupportscomputersrunningMacOS-X,Unix,orWindows,isdistributedfreeofcharge,andincludessourcecode.VMDisdesignedforthevisualizationandanalysisofbiologicalsystemssuchasproteins,nucleicacids,lipidbilayerassemblies,etc

22、.Itmaybeusedtoviewmoregeneralmolecules,asVMDcanreadstandardProteinDataBank(PDB)filesanddisplaythecontainedstructure.VMDprovidesawidevarietyofmethodsforrenderingandcoloringamolecule:simplepointsandlines,CPKspheresandcylinders,licoricebonds,backbonetubesandribbons,cartoondrawings,andothers.VMDcanbeuse

23、dtoanimateandanalyzethetrajectoryofamoleculardynamics(MD)simulation.Inparticular,VMDcanactasagraphicalfrontendforanexternalMDprogrambydisplayingandanimatingamoleculeundergoingsimulationonaremotecomputer.VMDusesOpenGLtoprovidehighperformance3-Dmoleculargraphics【相关链接】RasMol:3D分子构造显示程序PDB文件显示程序KineMage

24、美国伊利诺依大学：理论生物物理学研究组JMV(Java分子可视化工具)ProtoMol(分子动力学并行计算软件)ORAC(用于模拟溶剂化生物分子的分子动力学计算程序,意大利fo罗伦萨大学)【URL】httpchim.unifi.it/orac/【作者】MassimoMarchiandP.Procacci【语言版本】English【操作系统】UNIX【收费情况】免费【用处】ORACisaprogramforrunningclassicalsimulationsofbiomolecules.SimulationscanbecarriedoutintheNVE,NPT,NHP,andNVTtherm

25、odynamicensembles.Theintegrationoftheequationsofmotioninanyensemblecanbecarriedoutwithther-RESPAmultipletimestepintegratorandelectrostaticinteractionscanbehandledwiththeSmoothParticleMeshEwaldmethod.【备注】AparallelversionofORAC4.0(MPI/T3E)isavailableuponrequestto:MassimoMarchiSectiondeBiophysiquedesPr

26、oteinesetdesMembranes,DBCM,DSV,CEA,CentredEtudes,Saclay,91191Gif-sur-YvetteCedex,FRANCEVirtualMolecularDynamicsLaboratory(分子动力学软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./vmdl/index.【作者】AmitBansil,LidiaBraunstein【语言版本】English【收费情况】免费【用处】TheVirtualMolecularDynamicsLaboratoryenablesthestudenttovis

27、ualizeatomicmotion,manipulateatomicinteractions,andquantitativelyinvestigatetheresultingmacroscopicpropertiesofbiological,chemical,andphysicalsystems.TheVirtualLaboratoryisasuiteofresearch-basedmoleculardynamicssoftwaretoolsandproject-basedcurriculumguides.Thesoftwaretoolsare:SimpleMolecularDynamics

28、(SMD),UniversalMolecularDynamics,andWater.【相关链接】美国波士顿大学聚合物研究中心(可视化模拟)DL_POLY(分子动力学模拟软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./msi/software/DL_POLY/【作者】W.SmithandT.R.Forester【语言版本】English【收费情况】免费DL_POLYissuppliedtoindividualsunderalicenceandisfreeofcosttoacademicscientistspursuingscientificrese

29、archofanon-commercialnature.Agrouplicenceisalsoavailableforacademicresearchgroups.Allrecipientsofthecodemustfirstagreetothetermsofthelicence.CommercialorganisationsinterestedinacquiringthepackageshouldapproachDr.W.SmithatDaresburyLaboratoryinthefirstinstance.DaresburyLaboratoryisthesolecentrefordist

30、ributionofthepackage.【用处】DL_POLYisageneralpurposeserialandparallelmoleculardynamicssimulationpackageoriginallydevelopedatDaresburyLaboratorybyW.SmithandT.R.ForesterundertheauspicesoftheEngineeringandPhysicalSciencesResearchCouncil(EPSRC)fortheEPSRCsCollaborativeComputationalProjectfortheComputerSimu

31、lationofCondensedPhases(CCP5)andtheMolecularSimulationGroup(MSG)atDaresburyLaboratory.ThepackageisthepropertyoftheCentralLaboratoryoftheResearchCouncils.TwoversionsofDL_POLYarecurrentlyavailable.DL_POLY_2istheoriginalversionwhichhasbeenparallelisedusingtheReplicatedDatastrategyandisusefulforsimulati

32、onsofupto30,000atomson100processors.DL_POLY_3isaversionwhichusesDomainDecompositiontoachieveparallelismandissuitableforsimulationsoforder1millionatomson8-1024processors.DL_POLY(分子动力学模拟软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./msi/software/DL_POLY/【作者】W.SmithandT.R.Forester【语言版本】English【收费情况】免费

33、DL_POLYissuppliedtoindividualsunderalicenceandisfreeofcosttoacademicscientistspursuingscientificresearchofanon-commercialnature.Agrouplicenceisalsoavailableforacademicresearchgroups.Allrecipientsofthecodemustfirstagreetothetermsofthelicence.Commercialorganisationsinterestedinacquiringthepackageshoul

34、dapproachDr.W.SmithatDaresburyLaboratoryinthefirstinstance.DaresburyLaboratoryisthesolecentrefordistributionofthepackage.【用处】DL_POLYisageneralpurposeserialandparallelmoleculardynamicssimulationpackageoriginallydevelopedatDaresburyLaboratorybyW.SmithandT.R.ForesterundertheauspicesoftheEngineeringandP

35、hysicalSciencesResearchCouncil(EPSRC)fortheEPSRCsCollaborativeComputationalProjectfortheComputerSimulationofCondensedPhases(CCP5)andtheMolecularSimulationGroup(MSG)atDaresburyLaboratory.ThepackageisthepropertyoftheCentralLaboratoryoftheResearchCouncils.TwoversionsofDL_POLYarecurrentlyavailable.DL_PO

36、LY_2istheoriginalversionwhichhasbeenparallelisedusingtheReplicatedDatastrategyandisusefulforsimulationsofupto30,000atomson100processors.DL_POLY_3isaversionwhichusesDomainDecompositiontoachieveparallelismandissuitableforsimulationsoforder1millionatomson8-1024processors.PMDS(并行分子动力学模板库)【URL】httpstenci

37、l.koma.jaeri.go.jp/【作者】JapanAtomicEnergyResearchInstitute【语言版本】English【收费情况】免费【用处】ParallelMolecularDynamicsStencil(PMDS)isanassemblyofsubroutineprogramsforexecutingparallelshort-rangemolecular-dynamicssimulationsofsolids.PMDSiswritteninClanguageusingMPIforparallelization,andisdesignedtoseparateandco

38、ncealpartsoftheprogramsforparallelalgorithmssuchasinter-processorcommunicationssothatparallelprogrammingforforcecalculationcanbedoneinthesamewayasserialprogramming;itcanbeeasilyrevisedaccordingtophysicalmodels.MDRANGE(分子动力学计算ionranges)【URL】httpbeam.helsinki.fi/knordlun/mdh/mdh_program.【作者】KaiNordlun

39、d【语言版本】English【收费情况】免费【用处】TheofficialnameoftheprogramisMDRANGE.However,intheactualprogramfilestheshorter,moreconvenientnamemdh(abbreviatedfromMolecularDynamicsHigh-energy)isused.Bothnamestherefore(atleastfornow)meanexactlythesameprogram.Theprogramisamoleculardynamics(MD)simulationprogramtailoredfore

40、ffectivecalculationofionranges.Thewordeffectiveusedheremustbeunderstoodinthecontextofhigh-energymoleculardynamicscalculations.WhatitdoesCalculatesionrangesinsolidsCalculatesdepositedenergiesCalculatestheprimaryrecoilspectrumObtainingstoppingpowerspossibleindirectlyIonandsampleelementswhichcanbeused:

41、anyEnergyrangeinwhichcalculationcanbedone:roughly1eV/amu-10MeV/amuEnergyrangeinwhichuseisjustified:roughly100eV/amu-100keV/amuMDRANGE3.0:optionforPuska-Echenique-Nieminen-Ritchie(PENR)-electronicstoppingmodelSil00.Needschargedensityfilefromuser.MDRANGE3.0:optionforBrandt-Kitakawa(BK)-electronicstopp

42、ingmodel.Needschargedensityfilefromuser.【备注】KaiNordlundAcceleratorLaboratory,UniversityofHelsinki,P.O.BOX43,FIN-00014Helsinki,Finland(emailkai.nordlundhelsinki.fi)Car-Parrinello分子动力学(CPMD,ab-initio分子动力学计算软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff./【作者】JurgHutter【语言版本】English【操作系统】Unix/Linux【下载】h

43、ttpdocsj/doc/1385f5d0360cba1aa811daff./ftp.【收费情况】免费【用处】泛函：LDA，LSD，GGA，自由能密度泛函。孤立体系和周期边界体系的计算。对分子和晶体使用对称性。波函优化。几何优化与过渡态寻找。恒定能量，恒温，恒压的分子动力学。途径积分分子动力学。线性响应函数计算，NMR，Raman和IR。TDDFT计算激发态。多电子特性。周期体系的偶极矩。激发态的分子动力学。QM/MM方法。OpenMP并行化。【备注】ItsfirstversionwasdevelopedbyJurgHutteratIBMZurichResearchLaboratorystar

44、tingfromtheoriginalCar-Parrinellocodes.Duringtheyearsmanypeoplefromdiverseorganizationscontributedtothedevelopmentofthecodeandofitspseudopotentiallibrary:MicheleParrinello,JurgHutter,D.Marx,P.Focher,M.Tuckerman,W.Andreoni,A.Curioni,E.Fois,U.Roetlisberger,P.Giannozzi,T.Deutsch,A.Alavi,D.Sebastiani,A.

45、Laio,J.VandeVondele,A.Seitsonen,S.Billeterandothers.GROMACS(分子动力学软件)【URL】httpdocsj/doc/1385f5d0360cba1aa811daff.【作者】Dep.ofBiophysicalChemistry,GroningenUniversity【语言版本】C【操作系统】Unix【下载】httpdocsj/doc/1385f5d0360cba1aa811daff./download/index.php【收费情况】免费免费【用处】GROMACSisaversatilepackagetoperformmoleculard

46、ynamics,i.e.simulatetheNewtonianequationsofmotionforsystemswithhundredstomillionsofparticles.Itisprimarilydesignedforbiochemicalmoleculeslikeproteinsandlipidsthathavealotofcomplicatedbondedinteractions,butsinceGROMACSisextremelyfastatcalculatingthenonbondedinteractions(thatusuallydominatesimulations

47、)manygroupsarealsousingitforresearchonnon-biologicalsystems,e.g.polymers.GROMACSsupportsalltheusualalgorithmsyouexpectfromamodernmoleculardynamicsimplementation,buttherearealsoquiteafewfeaturesthatmakeitstandoutfromthecompetition:*GROMACSprovidesextremelyhighperformancecomparedtoallotherprograms.*GR

48、OMACSisuser-friendly,withtopologiesandparameterfileswrittenincleartextformat.*Thereisnoscriptinglanguage-allprogramsuseasimpleinterfacewithcommandlineoptionsforinputandoutputfiles.*Asthesimulationisproceeding,GROMACSwillcontinuouslytellyouhowfarithascome,andwhattimeanddateitexpectstobefinished.*BothruninputfilesandtrajectoriesareindependentofhardwareendianandcanthusbereadbyanyversionGROMACS,evenifitwascompiledusingadifferentfloating-pointprecisi